Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille
--- a/ChangeLog
+++ b/ChangeLog
+Stacks 2.41 - July 8, 2019
+--------------------------
+    Feature: populations: calculates haplotype-based Dxy (Nei, 1987) and provides for smoothing if a 
+             reference genome is available.
+    Feature: populations: re-implemented full sequence export for phylip format, including partitioning information.
+
+Stacks 2.4 - May 9, 2019
+------------------------
+    Feature: populations: re-implemented HZAR export.
+    Feature: added reporting code to detect issues with inconsistent versions of libz on a host system
+             causing Stacks components to fail to open compressed files.
+    Feature: gstacks: improved PCR duplicate reporting to be per-sample.
+    Bugfix:  populations: fixed an issues where the basepair position of a small number of loci was reported
+                          incorrectly -- they were shifted by a small, fixed offset.
+
+Stacks 2.3 - Jan 11, 2019
+--------------------------
+    Feature: populations: Backwards-compatibly worked on filtering options; added long names for -r and -p and
+             added --min-samples-overall and --filter-haplotype-wise.
+    Feature: populations: Implemented --treemix.
+    Feature: gstacks: Improved RAD-loci reference sequences around the end of forward (restriction site-bound) reads.
+    Feature: gstacks: Improved the way 2-microsatelittes are dealt with.
+    Feature: gstacks: Changed the default value for --var-alpha from 0.05 to 0.01 (--gt-alpha is unchanged at 0.05).
+    Feature: gstacks: Improved PCR duplicates-related log information (distribution of clone sizes).
+    Feature: gstacks: Added an option to save read alignments (--write-alignments).
+    Feature: Backwards-compatibly switched to hyphens in command line options (underscores remain accepted
+             where they previously were).
+    Feature: cstacks/sstacks now report an error when the disk becomes full.
+
+	2.3b - Jan 23, 2019
+	----------
+	Bugfix: Fixed some limit cases causing an abort at gstacks.cc:1752.
+	Bugfix: Fixed some limit cases causing an abort at debruijn.cc:60.
+	Bugfix: Fixed some limit cases apparently causing an infinite loop in the de Bruijn code.
+	Bugfix: Restored compilation with the oldest C++11 GCC versions (4.9 and 5.0).
+
+	2.3c - Feb 27, 2019
+	---------
+	Bugfix: Fixed assert failure at gstacks.cc:1171 (corrected with a return on gstacks.cc:1126)
+	Bugfix: inadvertantly compiling out BAM support from process_radtags due to the removal of the HAVE_BAM
+                config option, which occurred when we moved the BAM library internally to Stacks.
+	Bugfix: corrected infinite loop in populations when --write-single-snp and -r were enabled.
+        Bugfix: correct missing comment marker in population's FASTA exports and missing ']' character in FASTA comments.
+
+	2.3d - Feb 28, 2019
+	---------
+	Bugfix: the snps_per_loc_postfilters distribution in the populations.log.distrib file was slightly off due to counting
+                the number of SNPs at loci where despite SNP objects present at the locus, all sites were fixed in the
+	        focal populations.
+	Bugfix: Some haplotypes could pass through the filter, even after particular SNPs were filtered from them.
+	Bufgix: Corrected the samples per locus and absent-samples per locus distributions from populations. 
+
+	2.3e - Mar 20, 2019
+	---------
+	Bugfix: the --write-random-snp flag was causing an infinite loop in populations.
+
 Stacks 2.2 - Aug 22, 2018
 --------------------------
    Feature: Added the --bestrad flag to process_radtags. When used it will look for reads that need transposed
             before they are processed.
    Feature: gstacks: New option --max-debrujin-reads to control the construction of the de Bruijn graph; replaces
             --min-kmer-freq which is now deprecated
+    Bugfix: Fixed a breaking circumstantial segmentation fault in populations
    Bugfix: Added run number to output FASTQ headers in process_radtags to make sure read IDs are always unique.

 Stacks 2.1 - June 25, 2018

--- a/Makefile.am
+++ b/Makefile.am
@@ -89,22 +89,11 @@ dist_bin_SCRIPTS = scripts/denovo_map.pl scripts/ref_map.pl \

 dist_noinst_SCRIPTS = autogen.sh scripts/extract_interpop_chars.pl scripts/convert_stacks.pl

-nobase_pkgdata_DATA = sql/mysql.cnf.dist sql/catalog_index.sql sql/stacks.sql sql/tag_index.sql sql/chr_index.sql \
-	php/CatalogClass.php php/annotate_marker.php php/constants.php.dist php/index.php php/tags.php php/tag.php \
-	php/Locus.php php/catalog.php php/correct_genotypes.php php/correct_genotype.php php/export_batch.php php/last_modified.php  \
-	php/version.php php/catalog_genotypes.php php/db_functions.php php/header.php php/samples.php \
-	php/stacks_functions.php php/view_sequence.php php/sequence_blast.php \
-	php/pop_view.php php/sumstat_view.php php/hapstat_view.php php/fst_view.php php/phist_view.php php/stack_view.php \
-	php/population_view.js php/ajax.js php/annotate.js php/stacks.js php/export.js php/stacks.css \
-	php/images/caret-d.png php/images/caret-u.png php/images/excel_icon.png php/images/l-arrow-disabled.png \
-	php/images/l-arrow.png php/images/r-arrow-disabled.png php/images/r-arrow.png php/images/stacks_bg.png \
-	php/images/stacks_logo_rev_small.png
-
 LOG_DRIVER = env AM_TAP_AWK='$(AWK)' $(SHELL) $(abs_top_srcdir)/tests/tap-driver.sh

 TESTS = tests/process_radtags.t tests/kmer_filter.t tests/ustacks.t tests/pstacks.t

-EXTRA_DIST = $(nobase_pkgdata_DATA) LICENSE INSTALL README ChangeLog $(TESTS)
+EXTRA_DIST = LICENSE INSTALL README ChangeLog $(TESTS)

 pkglocalstatedir = $(localstatedir)/$(PACKAGE)

@@ -118,11 +107,6 @@ install-data-hook:
 	sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,$(bindir)/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/ref_map.pl > $(DESTDIR)$(bindir)/ref_map.pl.subst
 	mv $(DESTDIR)$(bindir)/ref_map.pl.subst $(DESTDIR)$(bindir)/ref_map.pl
 	chmod +x $(DESTDIR)$(bindir)/ref_map.pl
-	sed -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' -e 's,_BINDIR_,$(bindir)/,g' \
-		$(DESTDIR)$(pkgdatadir)/php/constants.php.dist > $(DESTDIR)$(pkgdatadir)/php/constants.php.dist.subst
-	mv $(DESTDIR)$(pkgdatadir)/php/constants.php.dist.subst $(DESTDIR)$(pkgdatadir)/php/constants.php.dist
-	echo $(VERSION) > $(DESTDIR)$(pkgdatadir)/php/version.php
-	$(install_sh) -d -m 755 $(DESTDIR)$(pkgdatadir)/php/export
 	sed -i.bkp -e 's,_VERSION_,$(VERSION),' $(DESTDIR)$(bindir)/stacks-integrate-alignments
 	rm -f $(DESTDIR)$(bindir)/stacks-integrate-alignments.bkp
 	chmod +x $(DESTDIR)$(bindir)/stacks-integrate-alignments

--- a/Makefile.in
+++ b/Makefile.in
-# Makefile.in generated by automake 1.15 from Makefile.am.
+# Makefile.in generated by automake 1.13.4 from Makefile.am.
 # @configure_input@

-# Copyright (C) 1994-2014 Free Software Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.

 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -16,19 +16,8 @@



-
 VPATH = @srcdir@
-am__is_gnu_make = { \
-  if test -z '$(MAKELEVEL)'; then \
-    false; \
-  elif test -n '$(MAKE_HOST)'; then \
-    true; \
-  elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
-    true; \
-  else \
-    false; \
-  fi; \
-}
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
 am__make_running_with_option = \
  case $${target_option-} in \
      ?) ;; \
@@ -95,14 +84,20 @@ bin_PROGRAMS = ustacks$(EXEEXT) cstacks$(EXEEXT) sstacks$(EXEEXT) \
 	populations$(EXEEXT) phasedstacks$(EXEEXT) tsv2bam$(EXEEXT) \
 	gstacks$(EXEEXT)
 subdir = .
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
+	$(top_srcdir)/configure $(am__configure_deps) \
+	$(srcdir)/config.h.in $(dist_bin_SCRIPTS) \
+	$(dist_noinst_SCRIPTS) $(top_srcdir)/config/depcomp \
+	$(top_srcdir)/config/test-driver ChangeLog INSTALL README \
+	config/ar-lib config/compile config/depcomp config/install-sh \
+	config/missing $(top_srcdir)/config/ar-lib \
+	$(top_srcdir)/config/compile $(top_srcdir)/config/install-sh \
+	$(top_srcdir)/config/missing
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
 am__aclocal_m4_deps = $(top_srcdir)/acinclude.m4 \
 	$(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
-DIST_COMMON = $(srcdir)/Makefile.am $(top_srcdir)/configure \
-	$(am__configure_deps) $(dist_bin_SCRIPTS) \
-	$(dist_noinst_SCRIPTS) $(am__DIST_COMMON)
 am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \
 configure.lineno config.status.lineno
 mkinstalldirs = $(install_sh) -d
@@ -142,8 +137,7 @@ am_libpop_a_OBJECTS = src/export_formats.$(OBJEXT) \
 	src/genotype_dictionaries.$(OBJEXT) src/PopSum.$(OBJEXT) \
 	src/Hwp.$(OBJEXT)
 libpop_a_OBJECTS = $(am_libpop_a_OBJECTS)
-am__installdirs = "$(DESTDIR)$(bindir)" "$(DESTDIR)$(bindir)" \
-	"$(DESTDIR)$(pkgdatadir)"
+am__installdirs = "$(DESTDIR)$(bindir)" "$(DESTDIR)$(bindir)"
 PROGRAMS = $(bin_PROGRAMS)
 am_clone_filter_OBJECTS = src/clone_filter.$(OBJEXT)
 clone_filter_OBJECTS = $(am_clone_filter_OBJECTS)
@@ -279,7 +273,6 @@ am__can_run_installinfo = \
    n|no|NO) false;; \
    *) (install-info --version) >/dev/null 2>&1;; \
  esac
-DATA = $(nobase_pkgdata_DATA)
 RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive	\
  distclean-recursive maintainer-clean-recursive
 am__recursive_targets = \
@@ -485,12 +478,6 @@ TEST_LOG_DRIVER = $(SHELL) $(top_srcdir)/config/test-driver
 TEST_LOG_COMPILE = $(TEST_LOG_COMPILER) $(AM_TEST_LOG_FLAGS) \
 	$(TEST_LOG_FLAGS)
 DIST_SUBDIRS = $(SUBDIRS)
-am__DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/config.h.in \
-	$(top_srcdir)/config/ar-lib $(top_srcdir)/config/compile \
-	$(top_srcdir)/config/depcomp $(top_srcdir)/config/install-sh \
-	$(top_srcdir)/config/missing $(top_srcdir)/config/test-driver \
-	ChangeLog INSTALL README config/ar-lib config/compile \
-	config/depcomp config/install-sh config/missing
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 distdir = $(PACKAGE)-$(VERSION)
 top_distdir = $(distdir)
@@ -621,7 +608,6 @@ pdfdir = @pdfdir@
 prefix = @prefix@
 program_transform_name = @program_transform_name@
 psdir = @psdir@
-runstatedir = @runstatedir@
 sbindir = @sbindir@
 sharedstatedir = @sharedstatedir@
 srcdir = @srcdir@
@@ -710,20 +696,9 @@ dist_bin_SCRIPTS = scripts/denovo_map.pl scripts/ref_map.pl \
 	scripts/stacks-integrate-alignments scripts/stacks-dist-extract scripts/stacks-gdb # scripts/denovo_map.py

 dist_noinst_SCRIPTS = autogen.sh scripts/extract_interpop_chars.pl scripts/convert_stacks.pl
-nobase_pkgdata_DATA = sql/mysql.cnf.dist sql/catalog_index.sql sql/stacks.sql sql/tag_index.sql sql/chr_index.sql \
-	php/CatalogClass.php php/annotate_marker.php php/constants.php.dist php/index.php php/tags.php php/tag.php \
-	php/Locus.php php/catalog.php php/correct_genotypes.php php/correct_genotype.php php/export_batch.php php/last_modified.php  \
-	php/version.php php/catalog_genotypes.php php/db_functions.php php/header.php php/samples.php \
-	php/stacks_functions.php php/view_sequence.php php/sequence_blast.php \
-	php/pop_view.php php/sumstat_view.php php/hapstat_view.php php/fst_view.php php/phist_view.php php/stack_view.php \
-	php/population_view.js php/ajax.js php/annotate.js php/stacks.js php/export.js php/stacks.css \
-	php/images/caret-d.png php/images/caret-u.png php/images/excel_icon.png php/images/l-arrow-disabled.png \
-	php/images/l-arrow.png php/images/r-arrow-disabled.png php/images/r-arrow.png php/images/stacks_bg.png \
-	php/images/stacks_logo_rev_small.png
-
 LOG_DRIVER = env AM_TAP_AWK='$(AWK)' $(SHELL) $(abs_top_srcdir)/tests/tap-driver.sh
 TESTS = tests/process_radtags.t tests/kmer_filter.t tests/ustacks.t tests/pstacks.t
-EXTRA_DIST = $(nobase_pkgdata_DATA) LICENSE INSTALL README ChangeLog $(TESTS)
+EXTRA_DIST = LICENSE INSTALL README ChangeLog $(TESTS)
 pkglocalstatedir = $(localstatedir)/$(PACKAGE)
 all: config.h
 	$(MAKE) $(AM_MAKEFLAGS) all-recursive
@@ -745,6 +720,7 @@ $(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
 	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign Makefile'; \
 	$(am__cd) $(top_srcdir) && \
 	  $(AUTOMAKE) --foreign Makefile
+.PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
 	  *config.status*) \
@@ -765,8 +741,8 @@ $(ACLOCAL_M4):  $(am__aclocal_m4_deps)
 $(am__aclocal_m4_deps):

 config.h: stamp-h1
-	@test -f $@ || rm -f stamp-h1
-	@test -f $@ || $(MAKE) $(AM_MAKEFLAGS) stamp-h1
+	@if test ! -f $@; then rm -f stamp-h1; else :; fi
+	@if test ! -f $@; then $(MAKE) $(AM_MAKEFLAGS) stamp-h1; else :; fi

 stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status
 	@rm -f stamp-h1
@@ -1066,30 +1042,6 @@ distclean-compile:
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
 @am__fastdepCXX_FALSE@	$(AM_V_CXX@am__nodep@)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
-install-nobase_pkgdataDATA: $(nobase_pkgdata_DATA)
-	@$(NORMAL_INSTALL)
-	@list='$(nobase_pkgdata_DATA)'; test -n "$(pkgdatadir)" || list=; \
-	if test -n "$$list"; then \
-	  echo " $(MKDIR_P) '$(DESTDIR)$(pkgdatadir)'"; \
-	  $(MKDIR_P) "$(DESTDIR)$(pkgdatadir)" || exit 1; \
-	fi; \
-	$(am__nobase_list) | while read dir files; do \
-	  xfiles=; for file in $$files; do \
-	    if test -f "$$file"; then xfiles="$$xfiles $$file"; \
-	    else xfiles="$$xfiles $(srcdir)/$$file"; fi; done; \
-	  test -z "$$xfiles" || { \
-	    test "x$$dir" = x. || { \
-	      echo " $(MKDIR_P) '$(DESTDIR)$(pkgdatadir)/$$dir'"; \
-	      $(MKDIR_P) "$(DESTDIR)$(pkgdatadir)/$$dir"; }; \
-	    echo " $(INSTALL_DATA) $$xfiles '$(DESTDIR)$(pkgdatadir)/$$dir'"; \
-	    $(INSTALL_DATA) $$xfiles "$(DESTDIR)$(pkgdatadir)/$$dir" || exit $$?; }; \
-	done
-
-uninstall-nobase_pkgdataDATA:
-	@$(NORMAL_UNINSTALL)
-	@list='$(nobase_pkgdata_DATA)'; test -n "$(pkgdatadir)" || list=; \
-	$(am__nobase_strip_setup); files=`$(am__nobase_strip)`; \
-	dir='$(DESTDIR)$(pkgdatadir)'; $(am__uninstall_files_from_dir)

 # This directory's subdirectories are mostly independent; you can cd
 # into them and run 'make' without going through this Makefile.
@@ -1227,7 +1179,7 @@ $(TEST_SUITE_LOG): $(TEST_LOGS)
 	if test -n "$$am__remaking_logs"; then \
 	  echo "fatal: making $(TEST_SUITE_LOG): possible infinite" \
 	       "recursion detected" >&2; \
-	elif test -n "$$redo_logs"; then \
+	else \
 	  am__remaking_logs=yes $(MAKE) $(AM_MAKEFLAGS) $$redo_logs; \
 	fi; \
 	if $(am__make_dryrun); then :; else \
@@ -1462,16 +1414,10 @@ dist-xz: distdir
 	$(am__post_remove_distdir)

 dist-tarZ: distdir
-	@echo WARNING: "Support for distribution archives compressed with" \
-		       "legacy program 'compress' is deprecated." >&2
-	@echo WARNING: "It will be removed altogether in Automake 2.0" >&2
 	tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z
 	$(am__post_remove_distdir)

 dist-shar: distdir
-	@echo WARNING: "Support for shar distribution archives is" \
-	               "deprecated." >&2
-	@echo WARNING: "It will be removed altogether in Automake 2.0" >&2
 	shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
 	$(am__post_remove_distdir)

@@ -1506,17 +1452,16 @@ distcheck: dist
 	esac
 	chmod -R a-w $(distdir)
 	chmod u+w $(distdir)
-	mkdir $(distdir)/_build $(distdir)/_build/sub $(distdir)/_inst
+	mkdir $(distdir)/_build $(distdir)/_inst
 	chmod a-w $(distdir)
 	test -d $(distdir)/_build || exit 0; \
 	dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
 	  && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
 	  && am__cwd=`pwd` \
-	  && $(am__cd) $(distdir)/_build/sub \
-	  && ../../configure \
+	  && $(am__cd) $(distdir)/_build \
+	  && ../configure --srcdir=.. --prefix="$$dc_install_base" \
 	    $(AM_DISTCHECK_CONFIGURE_FLAGS) \
 	    $(DISTCHECK_CONFIGURE_FLAGS) \
-	    --srcdir=../.. --prefix="$$dc_install_base" \
 	  && $(MAKE) $(AM_MAKEFLAGS) \
 	  && $(MAKE) $(AM_MAKEFLAGS) dvi \
 	  && $(MAKE) $(AM_MAKEFLAGS) check \
@@ -1572,10 +1517,10 @@ distcleancheck: distclean
 check-am: all-am
 	$(MAKE) $(AM_MAKEFLAGS) check-TESTS
 check: check-recursive
-all-am: Makefile $(LIBRARIES) $(PROGRAMS) $(SCRIPTS) $(DATA) config.h
+all-am: Makefile $(LIBRARIES) $(PROGRAMS) $(SCRIPTS) config.h
 installdirs: installdirs-recursive
 installdirs-am:
-	for dir in "$(DESTDIR)$(bindir)" "$(DESTDIR)$(bindir)" "$(DESTDIR)$(pkgdatadir)"; do \
+	for dir in "$(DESTDIR)$(bindir)" "$(DESTDIR)$(bindir)"; do \
 	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
 	done
 install: install-recursive
@@ -1637,7 +1582,7 @@ info: info-recursive

 info-am:

-install-data-am: install-nobase_pkgdataDATA
+install-data-am:
 	@$(NORMAL_INSTALL)
 	$(MAKE) $(AM_MAKEFLAGS) install-data-hook
 install-dvi: install-dvi-recursive
@@ -1685,8 +1630,7 @@ ps: ps-recursive

 ps-am:

-uninstall-am: uninstall-binPROGRAMS uninstall-dist_binSCRIPTS \
-	uninstall-nobase_pkgdataDATA
+uninstall-am: uninstall-binPROGRAMS uninstall-dist_binSCRIPTS
 	@$(NORMAL_INSTALL)
 	$(MAKE) $(AM_MAKEFLAGS) uninstall-hook
 .MAKE: $(am__recursive_targets) all check-am install-am \
@@ -1704,16 +1648,13 @@ uninstall-am: uninstall-binPROGRAMS uninstall-dist_binSCRIPTS \
 	install-data-am install-data-hook install-dist_binSCRIPTS \
 	install-dvi install-dvi-am install-exec install-exec-am \
 	install-html install-html-am install-info install-info-am \
-	install-man install-nobase_pkgdataDATA install-pdf \
-	install-pdf-am install-ps install-ps-am install-strip \
-	installcheck installcheck-am installdirs installdirs-am \
-	maintainer-clean maintainer-clean-generic mostlyclean \
-	mostlyclean-compile mostlyclean-generic pdf pdf-am ps ps-am \
-	recheck tags tags-am uninstall uninstall-am \
-	uninstall-binPROGRAMS uninstall-dist_binSCRIPTS uninstall-hook \
-	uninstall-nobase_pkgdataDATA
-
-.PRECIOUS: Makefile
+	install-man install-pdf install-pdf-am install-ps \
+	install-ps-am install-strip installcheck installcheck-am \
+	installdirs installdirs-am maintainer-clean \
+	maintainer-clean-generic mostlyclean mostlyclean-compile \
+	mostlyclean-generic pdf pdf-am ps ps-am recheck tags tags-am \
+	uninstall uninstall-am uninstall-binPROGRAMS \
+	uninstall-dist_binSCRIPTS uninstall-hook


 debug:
@@ -1726,11 +1667,6 @@ install-data-hook:
 	sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,$(bindir)/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/ref_map.pl > $(DESTDIR)$(bindir)/ref_map.pl.subst
 	mv $(DESTDIR)$(bindir)/ref_map.pl.subst $(DESTDIR)$(bindir)/ref_map.pl
 	chmod +x $(DESTDIR)$(bindir)/ref_map.pl
-	sed -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' -e 's,_BINDIR_,$(bindir)/,g' \
-		$(DESTDIR)$(pkgdatadir)/php/constants.php.dist > $(DESTDIR)$(pkgdatadir)/php/constants.php.dist.subst
-	mv $(DESTDIR)$(pkgdatadir)/php/constants.php.dist.subst $(DESTDIR)$(pkgdatadir)/php/constants.php.dist
-	echo $(VERSION) > $(DESTDIR)$(pkgdatadir)/php/version.php
-	$(install_sh) -d -m 755 $(DESTDIR)$(pkgdatadir)/php/export
 	sed -i.bkp -e 's,_VERSION_,$(VERSION),' $(DESTDIR)$(bindir)/stacks-integrate-alignments
 	rm -f $(DESTDIR)$(bindir)/stacks-integrate-alignments.bkp
 	chmod +x $(DESTDIR)$(bindir)/stacks-integrate-alignments

--- a/aclocal.m4
+++ b/aclocal.m4
-# generated automatically by aclocal 1.15 -*- Autoconf -*-
+# generated automatically by aclocal 1.13.4 -*- Autoconf -*-

-# Copyright (C) 1996-2014 Free Software Foundation, Inc.
+# Copyright (C) 1996-2013 Free Software Foundation, Inc.

 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -20,7 +20,7 @@ You have another version of autoconf.  It may work, but is not guaranteed to.
 If you have problems, you may need to regenerate the build system entirely.
 To do so, use the procedure documented by the package, typically 'autoreconf'.])])

-# Copyright (C) 2002-2014 Free Software Foundation, Inc.
+# Copyright (C) 2002-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -32,10 +32,10 @@ To do so, use the procedure documented by the package, typically 'autoreconf'.])
 # generated from the m4 files accompanying Automake X.Y.
 # (This private macro should not be called outside this file.)
 AC_DEFUN([AM_AUTOMAKE_VERSION],
-[am__api_version='1.15'
+[am__api_version='1.13'
 dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to
 dnl require some minimum version.  Point them to the right macro.
-m4_if([$1], [1.15], [],
+m4_if([$1], [1.13.4], [],
      [AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
 ])

@@ -51,12 +51,12 @@ m4_define([_AM_AUTOCONF_VERSION], [])
 # Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced.
 # This function is AC_REQUIREd by AM_INIT_AUTOMAKE.
 AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
-[AM_AUTOMAKE_VERSION([1.15])dnl
+[AM_AUTOMAKE_VERSION([1.13.4])dnl
 m4_ifndef([AC_AUTOCONF_VERSION],
  [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
 _AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])

-# Copyright (C) 2011-2014 Free Software Foundation, Inc.
+# Copyright (C) 2011-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -76,8 +76,7 @@ AC_CHECK_TOOLS([AR], [ar lib "link -lib"], [false])
 : ${AR=ar}

 AC_CACHE_CHECK([the archiver ($AR) interface], [am_cv_ar_interface],
-  [AC_LANG_PUSH([C])
-   am_cv_ar_interface=ar
+  [am_cv_ar_interface=ar
   AC_COMPILE_IFELSE([AC_LANG_SOURCE([[int some_variable = 0;]])],
     [am_ar_try='$AR cru libconftest.a conftest.$ac_objext >&AS_MESSAGE_LOG_FD'
      AC_TRY_EVAL([am_ar_try])
@@ -94,7 +93,7 @@ AC_CACHE_CHECK([the archiver ($AR) interface], [am_cv_ar_interface],
      fi
      rm -f conftest.lib libconftest.a
     ])
-   AC_LANG_POP([C])])
+   ])

 case $am_cv_ar_interface in
 ar)
@@ -118,7 +117,7 @@ AC_SUBST([AR])dnl

 # AM_AUX_DIR_EXPAND                                         -*- Autoconf -*-

-# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+# Copyright (C) 2001-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -163,14 +162,15 @@ AC_SUBST([AR])dnl
 # configured tree to be moved without reconfiguration.

 AC_DEFUN([AM_AUX_DIR_EXPAND],
-[AC_REQUIRE([AC_CONFIG_AUX_DIR_DEFAULT])dnl
-# Expand $ac_aux_dir to an absolute path.
-am_aux_dir=`cd "$ac_aux_dir" && pwd`
+[dnl Rely on autoconf to set up CDPATH properly.
+AC_PREREQ([2.50])dnl
+# expand $ac_aux_dir to an absolute path
+am_aux_dir=`cd $ac_aux_dir && pwd`
 ])

 # AM_CONDITIONAL                                            -*- Autoconf -*-

-# Copyright (C) 1997-2014 Free Software Foundation, Inc.
+# Copyright (C) 1997-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -201,7 +201,7 @@ AC_CONFIG_COMMANDS_PRE(
 Usually this means the macro was only invoked conditionally.]])
 fi])])

-# Copyright (C) 1999-2014 Free Software Foundation, Inc.
+# Copyright (C) 1999-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -392,7 +392,7 @@ _AM_SUBST_NOTMAKE([am__nodep])dnl

 # Generate code to set up dependency tracking.              -*- Autoconf -*-

-# Copyright (C) 1999-2014 Free Software Foundation, Inc.
+# Copyright (C) 1999-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -468,7 +468,7 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],

 # Do all the work for Automake.                             -*- Autoconf -*-

-# Copyright (C) 1996-2014 Free Software Foundation, Inc.
+# Copyright (C) 1996-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -477,12 +477,6 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
 # This macro actually does too much.  Some checks are only needed if
 # your package does certain things.  But this isn't really a big deal.

-dnl Redefine AC_PROG_CC to automatically invoke _AM_PROG_CC_C_O.
-m4_define([AC_PROG_CC],
-m4_defn([AC_PROG_CC])
-[_AM_PROG_CC_C_O
-])
-
 # AM_INIT_AUTOMAKE(PACKAGE, VERSION, [NO-DEFINE])
 # AM_INIT_AUTOMAKE([OPTIONS])
 # -----------------------------------------------
@@ -558,8 +552,8 @@ AC_REQUIRE([AC_PROG_MKDIR_P])dnl
 # <http://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
 # <http://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
 AC_SUBST([mkdir_p], ['$(MKDIR_P)'])
-# We need awk for the "check" target (and possibly the TAP driver).  The
-# system "awk" is bad on some platforms.
+# We need awk for the "check" target.  The system "awk" is bad on
+# some platforms.
 AC_REQUIRE([AC_PROG_AWK])dnl
 AC_REQUIRE([AC_PROG_MAKE_SET])dnl
 AC_REQUIRE([AM_SET_LEADING_DOT])dnl
@@ -591,51 +585,6 @@ dnl macro is hooked onto _AC_COMPILER_EXEEXT early, see below.
 AC_CONFIG_COMMANDS_PRE(dnl
 [m4_provide_if([_AM_COMPILER_EXEEXT],
  [AM_CONDITIONAL([am__EXEEXT], [test -n "$EXEEXT"])])])dnl
-
-# POSIX will say in a future version that running "rm -f" with no argument
-# is OK; and we want to be able to make that assumption in our Makefile
-# recipes.  So use an aggressive probe to check that the usage we want is
-# actually supported "in the wild" to an acceptable degree.
-# See automake bug#10828.
-# To make any issue more visible, cause the running configure to be aborted
-# by default if the 'rm' program in use doesn't match our expectations; the
-# user can still override this though.
-if rm -f && rm -fr && rm -rf; then : OK; else
-  cat >&2 <<'END'
-Oops!
-
-Your 'rm' program seems unable to run without file operands specified
-on the command line, even when the '-f' option is present.  This is contrary
-to the behaviour of most rm programs out there, and not conforming with
-the upcoming POSIX standard: <http://austingroupbugs.net/view.php?id=542>
-
-Please tell bug-automake@gnu.org about your system, including the value
-of your $PATH and any error possibly output before this message.  This
-can help us improve future automake versions.
-
-END
-  if test x"$ACCEPT_INFERIOR_RM_PROGRAM" = x"yes"; then
-    echo 'Configuration will proceed anyway, since you have set the' >&2
-    echo 'ACCEPT_INFERIOR_RM_PROGRAM variable to "yes"' >&2
-    echo >&2
-  else
-    cat >&2 <<'END'
-Aborting the configuration process, to ensure you take notice of the issue.
-
-You can download and install GNU coreutils to get an 'rm' implementation
-that behaves properly: <http://www.gnu.org/software/coreutils/>.
-
-If you want to complete the configuration process using your problematic
-'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM
-to "yes", and re-run configure.
-
-END
-    AC_MSG_ERROR([Your 'rm' program is bad, sorry.])
-  fi
-fi
-dnl The trailing newline in this macro's definition is deliberate, for
-dnl backward compatibility and to allow trailing 'dnl'-style comments
-dnl after the AM_INIT_AUTOMAKE invocation. See automake bug#16841.
 ])

 dnl Hook into '_AC_COMPILER_EXEEXT' early to learn its expansion.  Do not
@@ -644,6 +593,7 @@ dnl mangled by Autoconf and run in a shell conditional statement.
 m4_define([_AC_COMPILER_EXEEXT],
 m4_defn([_AC_COMPILER_EXEEXT])[m4_provide([_AM_COMPILER_EXEEXT])])

+
 # When config.status generates a header, we must update the stamp-h file.
 # This file resides in the same directory as the config header
 # that is generated.  The stamp files are numbered to have different names.
@@ -665,7 +615,7 @@ for _am_header in $config_headers :; do
 done
 echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count])

-# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+# Copyright (C) 2001-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -676,7 +626,7 @@ echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_co
 # Define $install_sh.
 AC_DEFUN([AM_PROG_INSTALL_SH],
 [AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
-if test x"${install_sh+set}" != xset; then
+if test x"${install_sh}" != xset; then
  case $am_aux_dir in
  *\ * | *\	*)
    install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
@@ -686,7 +636,7 @@ if test x"${install_sh+set}" != xset; then
 fi
 AC_SUBST([install_sh])])

-# Copyright (C) 2003-2014 Free Software Foundation, Inc.
+# Copyright (C) 2003-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -707,7 +657,7 @@ AC_SUBST([am__leading_dot])])

 # Check to see how 'make' treats includes.	            -*- Autoconf -*-

-# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+# Copyright (C) 2001-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -755,9 +705,41 @@ AC_MSG_RESULT([$_am_result])
 rm -f confinc confmf
 ])

+# Copyright (C) 1999-2013 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# AM_PROG_CC_C_O
+# --------------
+# Like AC_PROG_CC_C_O, but changed for automake.
+AC_DEFUN([AM_PROG_CC_C_O],
+[AC_REQUIRE([AC_PROG_CC_C_O])dnl
+AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
+AC_REQUIRE_AUX_FILE([compile])dnl
+# FIXME: we rely on the cache variable name because
+# there is no other way.
+set dummy $CC
+am_cc=`echo $[2] | sed ['s/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/']`
+eval am_t=\$ac_cv_prog_cc_${am_cc}_c_o
+if test "$am_t" != yes; then
+   # Losing compiler, so override with the script.
+   # FIXME: It is wrong to rewrite CC.
+   # But if we don't then we get into trouble of one sort or another.
+   # A longer-term fix would be to have automake use am__CC in this case,
+   # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
+   CC="$am_aux_dir/compile $CC"
+fi
+dnl Make sure AC_PROG_CC is never called again, or it will override our
+dnl setting of CC.
+m4_define([AC_PROG_CC],
+          [m4_fatal([AC_PROG_CC cannot be called after AM_PROG_CC_C_O])])
+])
+
 # Fake the existence of programs that GNU maintainers use.  -*- Autoconf -*-

-# Copyright (C) 1997-2014 Free Software Foundation, Inc.
+# Copyright (C) 1997-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -796,7 +778,7 @@ fi

 # Helper functions for option handling.                     -*- Autoconf -*-

-# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+# Copyright (C) 2001-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -825,73 +807,9 @@ AC_DEFUN([_AM_SET_OPTIONS],
 AC_DEFUN([_AM_IF_OPTION],
 [m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])])

-# Copyright (C) 1999-2014 Free Software Foundation, Inc.
-#
-# This file is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# _AM_PROG_CC_C_O
-# ---------------
-# Like AC_PROG_CC_C_O, but changed for automake.  We rewrite AC_PROG_CC
-# to automatically call this.
-AC_DEFUN([_AM_PROG_CC_C_O],
-[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
-AC_REQUIRE_AUX_FILE([compile])dnl
-AC_LANG_PUSH([C])dnl
-AC_CACHE_CHECK(
-  [whether $CC understands -c and -o together],
-  [am_cv_prog_cc_c_o],
-  [AC_LANG_CONFTEST([AC_LANG_PROGRAM([])])
-  # Make sure it works both with $CC and with simple cc.
-  # Following AC_PROG_CC_C_O, we do the test twice because some
-  # compilers refuse to overwrite an existing .o file with -o,
-  # though they will create one.
-  am_cv_prog_cc_c_o=yes
-  for am_i in 1 2; do
-    if AM_RUN_LOG([$CC -c conftest.$ac_ext -o conftest2.$ac_objext]) \
-         && test -f conftest2.$ac_objext; then
-      : OK
-    else
-      am_cv_prog_cc_c_o=no
-      break
-    fi
-  done
-  rm -f core conftest*
-  unset am_i])
-if test "$am_cv_prog_cc_c_o" != yes; then
-   # Losing compiler, so override with the script.
-   # FIXME: It is wrong to rewrite CC.
-   # But if we don't then we get into trouble of one sort or another.
-   # A longer-term fix would be to have automake use am__CC in this case,
-   # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
-   CC="$am_aux_dir/compile $CC"
-fi
-AC_LANG_POP([C])])
-
-# For backward compatibility.
-AC_DEFUN_ONCE([AM_PROG_CC_C_O], [AC_REQUIRE([AC_PROG_CC])])
-
-# Copyright (C) 2001-2014 Free Software Foundation, Inc.
-#
-# This file is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# AM_RUN_LOG(COMMAND)
-# -------------------
-# Run COMMAND, save the exit status in ac_status, and log it.
-# (This has been adapted from Autoconf's _AC_RUN_LOG macro.)
-AC_DEFUN([AM_RUN_LOG],
-[{ echo "$as_me:$LINENO: $1" >&AS_MESSAGE_LOG_FD
-   ($1) >&AS_MESSAGE_LOG_FD 2>&AS_MESSAGE_LOG_FD
-   ac_status=$?
-   echo "$as_me:$LINENO: \$? = $ac_status" >&AS_MESSAGE_LOG_FD
-   (exit $ac_status); }])
-
 # Check to make sure that the build environment is sane.    -*- Autoconf -*-

-# Copyright (C) 1996-2014 Free Software Foundation, Inc.
+# Copyright (C) 1996-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -972,7 +890,7 @@ AC_CONFIG_COMMANDS_PRE(
 rm -f conftest.file
 ])

-# Copyright (C) 2009-2014 Free Software Foundation, Inc.
+# Copyright (C) 2009-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1032,7 +950,7 @@ AC_SUBST([AM_BACKSLASH])dnl
 _AM_SUBST_NOTMAKE([AM_BACKSLASH])dnl
 ])

-# Copyright (C) 2001-2014 Free Software Foundation, Inc.
+# Copyright (C) 2001-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1060,7 +978,7 @@ fi
 INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
 AC_SUBST([INSTALL_STRIP_PROGRAM])])

-# Copyright (C) 2006-2014 Free Software Foundation, Inc.
+# Copyright (C) 2006-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -1079,7 +997,7 @@ AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])

 # Check how to create a tarball.                            -*- Autoconf -*-

-# Copyright (C) 2004-2014 Free Software Foundation, Inc.
+# Copyright (C) 2004-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,

--- a/config.h.in
+++ b/config.h.in
@@ -89,6 +89,9 @@
 /* Define to 1 if the system has the type `_Bool'. */
 #undef HAVE__BOOL

+/* Define to 1 if your C compiler doesn't accept -c and -o together. */
+#undef NO_MINUS_C_MINUS_O
+
 /* Name of package */
 #undef PACKAGE


--- a/config/ar-lib
+++ b/config/ar-lib
@@ -4,7 +4,7 @@
 me=ar-lib
 scriptversion=2012-03-01.08; # UTC

-# Copyright (C) 2010-2014 Free Software Foundation, Inc.
+# Copyright (C) 2010-2013 Free Software Foundation, Inc.
 # Written by Peter Rosin <peda@lysator.liu.se>.
 #
 # This program is free software; you can redistribute it and/or modify

--- a/config/compile
+++ b/config/compile
@@ -3,7 +3,7 @@

 scriptversion=2012-10-14.11; # UTC

-# Copyright (C) 1999-2014 Free Software Foundation, Inc.
+# Copyright (C) 1999-2013 Free Software Foundation, Inc.
 # Written by Tom Tromey <tromey@cygnus.com>.
 #
 # This program is free software; you can redistribute it and/or modify

--- a/config/depcomp
+++ b/config/depcomp
@@ -3,7 +3,7 @@

 scriptversion=2013-05-30.07; # UTC

-# Copyright (C) 1999-2014 Free Software Foundation, Inc.
+# Copyright (C) 1999-2013 Free Software Foundation, Inc.

 # This program is free software; you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

--- a/config/install-sh
+++ b/config/install-sh
 #!/bin/sh
 # install - install a program, script, or datafile

-scriptversion=2014-09-12.12; # UTC
+scriptversion=2011-11-20.07; # UTC

 # This originates from X11R5 (mit/util/scripts/install.sh), which was
 # later released in X11R6 (xc/config/util/install.sh) with the
@@ -41,15 +41,19 @@ scriptversion=2014-09-12.12; # UTC
 # This script is compatible with the BSD install script, but was written
 # from scratch.

-tab='	'
 nl='
 '
-IFS=" $tab$nl"
+IFS=" ""	$nl"

-# Set DOITPROG to "echo" to test this script.
+# set DOITPROG to echo to test this script

+# Don't use :- since 4.3BSD and earlier shells don't like it.
 doit=${DOITPROG-}
-doit_exec=${doit:-exec}
+if test -z "$doit"; then
+  doit_exec=exec
+else
+  doit_exec=$doit
+fi

 # Put in absolute file names if you don't have them in your path;
 # or use environment vars.
@@ -64,6 +68,17 @@ mvprog=${MVPROG-mv}
 rmprog=${RMPROG-rm}
 stripprog=${STRIPPROG-strip}

+posix_glob='?'
+initialize_posix_glob='
+  test "$posix_glob" != "?" || {
+    if (set -f) 2>/dev/null; then
+      posix_glob=
+    else
+      posix_glob=:
+    fi
+  }
+'
+
 posix_mkdir=

 # Desired mode of installed file.
@@ -82,7 +97,7 @@ dir_arg=
 dst_arg=

 copy_on_change=false
-is_target_a_directory=possibly
+no_target_directory=

 usage="\
 Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
@@ -128,7 +143,8 @@ while test $# -ne 0; do

    -m) mode=$2
 	case $mode in
-          *' '* | *"$tab"* | *"$nl"* | *'*'* | *'?'* | *'['*)
+	  *' '* | *'	'* | *'
+'*	  | *'*'* | *'?'* | *'['*)
 	    echo "$0: invalid mode: $mode" >&2
 	    exit 1;;
 	esac
@@ -139,16 +155,14 @@ while test $# -ne 0; do

    -s) stripcmd=$stripprog;;

-    -t)
-        is_target_a_directory=always
-        dst_arg=$2
+    -t) dst_arg=$2
 	# Protect names problematic for 'test' and other utilities.
 	case $dst_arg in
 	  -* | [=\(\)!]) dst_arg=./$dst_arg;;
 	esac
 	shift;;

-    -T) is_target_a_directory=never;;
+    -T) no_target_directory=true;;

    --version) echo "$0 $scriptversion"; exit $?;;

@@ -163,16 +177,6 @@ while test $# -ne 0; do
  shift
 done

-# We allow the use of options -d and -T together, by making -d
-# take the precedence; this is for compatibility with GNU install.
-
-if test -n "$dir_arg"; then
-  if test -n "$dst_arg"; then
-    echo "$0: target directory not allowed when installing a directory." >&2
-    exit 1
-  fi
-fi
-
 if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then
  # When -d is used, all remaining arguments are directories to create.
  # When -t is used, the destination is already specified.
@@ -203,15 +207,6 @@ if test $# -eq 0; then
  exit 0
 fi

-if test -z "$dir_arg"; then
-  if test $# -gt 1 || test "$is_target_a_directory" = always; then
-    if test ! -d "$dst_arg"; then
-      echo "$0: $dst_arg: Is not a directory." >&2
-      exit 1
-    fi
-  fi
-fi
-
 if test -z "$dir_arg"; then
  do_exit='(exit $ret); exit $ret'
  trap "ret=129; $do_exit" 1
@@ -274,7 +269,7 @@ do
    # If destination is a directory, append the input filename; won't work
    # if double slashes aren't ignored.
    if test -d "$dst"; then
-      if test "$is_target_a_directory" = never; then
+      if test -n "$no_target_directory"; then
 	echo "$0: $dst_arg: Is a directory" >&2
 	exit 1
      fi
@@ -282,7 +277,33 @@ do
      dst=$dstdir/`basename "$src"`
      dstdir_status=0
    else
-      dstdir=`dirname "$dst"`
+      # Prefer dirname, but fall back on a substitute if dirname fails.
+      dstdir=`
+	(dirname "$dst") 2>/dev/null ||
+	expr X"$dst" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+	     X"$dst" : 'X\(//\)[^/]' \| \
+	     X"$dst" : 'X\(//\)$' \| \
+	     X"$dst" : 'X\(/\)' \| . 2>/dev/null ||
+	echo X"$dst" |
+	    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+		   s//\1/
+		   q
+		 }
+		 /^X\(\/\/\)[^/].*/{
+		   s//\1/
+		   q
+		 }
+		 /^X\(\/\/\)$/{
+		   s//\1/
+		   q
+		 }
+		 /^X\(\/\).*/{
+		   s//\1/
+		   q
+		 }
+		 s/.*/./; q'
+      `
+
      test -d "$dstdir"
      dstdir_status=$?
    fi
@@ -324,41 +345,34 @@ do
 	    # is incompatible with FreeBSD 'install' when (umask & 300) != 0.
 	    ;;
 	  *)
-            # $RANDOM is not portable (e.g. dash);  use it when possible to
-            # lower collision chance
 	    tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$
-            trap 'ret=$?; rmdir "$tmpdir/a/b" "$tmpdir/a" "$tmpdir" 2>/dev/null; exit $ret' 0
+	    trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0

-            # As "mkdir -p" follows symlinks and we work in /tmp possibly;  so
-            # create the $tmpdir first (and fail if unsuccessful) to make sure
-            # that nobody tries to guess the $tmpdir name.
 	    if (umask $mkdir_umask &&
-                $mkdirprog $mkdir_mode "$tmpdir" &&
-                exec $mkdirprog $mkdir_mode -p -- "$tmpdir/a/b") >/dev/null 2>&1
+		exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1
 	    then
 	      if test -z "$dir_arg" || {
 		   # Check for POSIX incompatibilities with -m.
 		   # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
 		   # other-writable bit of parent directory when it shouldn't.
 		   # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
-                   test_tmpdir="$tmpdir/a"
-                   ls_ld_tmpdir=`ls -ld "$test_tmpdir"`
+		   ls_ld_tmpdir=`ls -ld "$tmpdir"`
 		   case $ls_ld_tmpdir in
 		     d????-?r-*) different_mode=700;;
 		     d????-?--*) different_mode=755;;
 		     *) false;;
 		   esac &&
-                   $mkdirprog -m$different_mode -p -- "$test_tmpdir" && {
-                     ls_ld_tmpdir_1=`ls -ld "$test_tmpdir"`
+		   $mkdirprog -m$different_mode -p -- "$tmpdir" && {
+		     ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
 		     test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
 		   }
 		 }
 	      then posix_mkdir=:
 	      fi
-              rmdir "$tmpdir/a/b" "$tmpdir/a" "$tmpdir"
+	      rmdir "$tmpdir/d" "$tmpdir"
 	    else
 	      # Remove any dirs left behind by ancient mkdir implementations.
-              rmdir ./$mkdir_mode ./-p ./-- "$tmpdir" 2>/dev/null
+	      rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null
 	    fi
 	    trap '' 0;;
 	esac;;
@@ -382,12 +396,14 @@ do
 	*)  prefix='';;
      esac

+      eval "$initialize_posix_glob"
+
      oIFS=$IFS
      IFS=/
-      set -f
+      $posix_glob set -f
      set fnord $dstdir
      shift
-      set +f
+      $posix_glob set +f
      IFS=$oIFS

      prefixes=
@@ -458,10 +474,13 @@ do
    if $copy_on_change &&
       old=`LC_ALL=C ls -dlL "$dst"	2>/dev/null` &&
       new=`LC_ALL=C ls -dlL "$dsttmp"	2>/dev/null` &&
-       set -f &&
+
+       eval "$initialize_posix_glob" &&
+       $posix_glob set -f &&
       set X $old && old=:$2:$4:$5:$6 &&
       set X $new && new=:$2:$4:$5:$6 &&
-       set +f &&
+       $posix_glob set +f &&
+
       test "$old" = "$new" &&
       $cmpprog "$dst" "$dsttmp" >/dev/null 2>&1
    then

--- a/config/missing
+++ b/config/missing
 #! /bin/sh
 # Common wrapper for a few potentially missing GNU programs.

-scriptversion=2013-10-28.13; # UTC
+scriptversion=2012-06-26.16; # UTC

-# Copyright (C) 1996-2014 Free Software Foundation, Inc.
+# Copyright (C) 1996-2013 Free Software Foundation, Inc.
 # Originally written by Fran,cois Pinard <pinard@iro.umontreal.ca>, 1996.

 # This program is free software; you can redistribute it and/or modify
@@ -160,7 +160,7 @@ give_advice ()
      ;;
   autom4te*)
      echo "You might have modified some maintainer files that require"
-      echo "the 'autom4te' program to be rebuilt."
+      echo "the 'automa4te' program to be rebuilt."
      program_details 'autom4te'
      ;;
    bison*|yacc*)

--- a/config/test-driver
+++ b/config/test-driver
 #! /bin/sh
 # test-driver - basic testsuite driver script.

-scriptversion=2013-07-13.22; # UTC
+scriptversion=2012-06-27.10; # UTC

-# Copyright (C) 2011-2014 Free Software Foundation, Inc.
+# Copyright (C) 2011-2013 Free Software Foundation, Inc.
 #
 # This program is free software; you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -44,12 +44,13 @@ print_usage ()
 Usage:
  test-driver --test-name=NAME --log-file=PATH --trs-file=PATH
              [--expect-failure={yes|no}] [--color-tests={yes|no}]
-              [--enable-hard-errors={yes|no}] [--]
-              TEST-SCRIPT [TEST-SCRIPT-ARGUMENTS]
+              [--enable-hard-errors={yes|no}] [--] TEST-SCRIPT
 The '--test-name', '--log-file' and '--trs-file' options are mandatory.
 END
 }

+# TODO: better error handling in option parsing (in particular, ensure
+# TODO: $log_file, $trs_file and $test_name are defined).
 test_name= # Used for reporting.
 log_file=  # Where to save the output of the test script.
 trs_file=  # Where to save the metadata of the test run.
@@ -68,23 +69,10 @@ while test $# -gt 0; do
  --enable-hard-errors) enable_hard_errors=$2; shift;;
  --) shift; break;;
  -*) usage_error "invalid option: '$1'";;
-   *) break;;
  esac
  shift
 done

-missing_opts=
-test x"$test_name" = x && missing_opts="$missing_opts --test-name"
-test x"$log_file"  = x && missing_opts="$missing_opts --log-file"
-test x"$trs_file"  = x && missing_opts="$missing_opts --trs-file"
-if test x"$missing_opts" != x; then
-  usage_error "the following mandatory options are missing:$missing_opts"
-fi
-
-if test $# -eq 0; then
-  usage_error "missing argument"
-fi
-
 if test $color_tests = yes; then
  # Keep this in sync with 'lib/am/check.am:$(am__tty_colors)'.
  red='[0;31m' # Red.
@@ -106,14 +94,11 @@ trap "st=143; $do_exit" 15
 # Test script is run here.
 "$@" >$log_file 2>&1
 estatus=$?
-
 if test $enable_hard_errors = no && test $estatus -eq 99; then
-  tweaked_estatus=1
-else
-  tweaked_estatus=$estatus
+  estatus=1
 fi

-case $tweaked_estatus:$expect_failure in
+case $estatus:$expect_failure in
  0:yes) col=$red res=XPASS recheck=yes gcopy=yes;;
  0:*)   col=$grn res=PASS  recheck=no  gcopy=no;;
  77:*)  col=$blu res=SKIP  recheck=no  gcopy=yes;;
@@ -122,12 +107,6 @@ case $tweaked_estatus:$expect_failure in
  *:*)   col=$red res=FAIL  recheck=yes gcopy=yes;;
 esac

-# Report the test outcome and exit status in the logs, so that one can
-# know whether the test passed or failed simply by looking at the '.log'
-# file, without the need of also peaking into the corresponding '.trs'
-# file (automake bug#11814).
-echo "$res $test_name (exit status: $estatus)" >>$log_file
-
 # Report outcome to console.
 echo "${col}${res}${std}: $test_name"


--- a/configure
+++ b/configure
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for Stacks 2.2.
+# Generated by GNU Autoconf 2.69 for Stacks 2.41.
 #
 #
 # Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
@@ -577,8 +577,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='Stacks'
 PACKAGE_TARNAME='stacks'
-PACKAGE_VERSION='2.2'
-PACKAGE_STRING='Stacks 2.2'
+PACKAGE_VERSION='2.41'
+PACKAGE_STRING='Stacks 2.41'
 PACKAGE_BUGREPORT=''
 PACKAGE_URL=''

@@ -701,7 +701,6 @@ infodir
 docdir
 oldincludedir
 includedir
-runstatedir
 localstatedir
 sharedstatedir
 sysconfdir
@@ -778,7 +777,6 @@ datadir='${datarootdir}'
 sysconfdir='${prefix}/etc'
 sharedstatedir='${prefix}/com'
 localstatedir='${prefix}/var'
-runstatedir='${localstatedir}/run'
 includedir='${prefix}/include'
 oldincludedir='/usr/include'
 docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
@@ -1031,15 +1029,6 @@ do
  | -silent | --silent | --silen | --sile | --sil)
    silent=yes ;;

-  -runstatedir | --runstatedir | --runstatedi | --runstated \
-  | --runstate | --runstat | --runsta | --runst | --runs \
-  | --run | --ru | --r)
-    ac_prev=runstatedir ;;
-  -runstatedir=* | --runstatedir=* | --runstatedi=* | --runstated=* \
-  | --runstate=* | --runstat=* | --runsta=* | --runst=* | --runs=* \
-  | --run=* | --ru=* | --r=*)
-    runstatedir=$ac_optarg ;;
-
  -sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb)
    ac_prev=sbindir ;;
  -sbindir=* | --sbindir=* | --sbindi=* | --sbind=* | --sbin=* \
@@ -1177,7 +1166,7 @@ fi
 for ac_var in	exec_prefix prefix bindir sbindir libexecdir datarootdir \
 		datadir sysconfdir sharedstatedir localstatedir includedir \
 		oldincludedir docdir infodir htmldir dvidir pdfdir psdir \
-		libdir localedir mandir runstatedir
+		libdir localedir mandir
 do
  eval ac_val=\$$ac_var
  # Remove trailing slashes.
@@ -1290,7 +1279,7 @@ if test "$ac_init_help" = "long"; then
  # Omit some internal or obsolete options to make the list less imposing.
  # This message is too long to be a string in the A/UX 3.1 sh.
  cat <<_ACEOF
-\`configure' configures Stacks 2.2 to adapt to many kinds of systems.
+\`configure' configures Stacks 2.41 to adapt to many kinds of systems.

 Usage: $0 [OPTION]... [VAR=VALUE]...

@@ -1330,7 +1319,6 @@ Fine tuning of the installation directories:
  --sysconfdir=DIR        read-only single-machine data [PREFIX/etc]
  --sharedstatedir=DIR    modifiable architecture-independent data [PREFIX/com]
  --localstatedir=DIR     modifiable single-machine data [PREFIX/var]
-  --runstatedir=DIR       modifiable per-process data [LOCALSTATEDIR/run]
  --libdir=DIR            object code libraries [EPREFIX/lib]
  --includedir=DIR        C header files [PREFIX/include]
  --oldincludedir=DIR     C header files for non-gcc [/usr/include]
@@ -1357,7 +1345,7 @@ fi

 if test -n "$ac_init_help"; then
  case $ac_init_help in
-     short | recursive ) echo "Configuration of Stacks 2.2:";;
+     short | recursive ) echo "Configuration of Stacks 2.41:";;
   esac
  cat <<\_ACEOF

@@ -1451,7 +1439,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
  cat <<\_ACEOF
-Stacks configure 2.2
+Stacks configure 2.41
 generated by GNU Autoconf 2.69

 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1950,7 +1938,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.

-It was created by Stacks $as_me 2.2, which was
+It was created by Stacks $as_me 2.41, which was
 generated by GNU Autoconf 2.69.  Invocation command line was

  $ $0 $@
@@ -2327,7 +2315,7 @@ ac_config_sub="$SHELL $ac_aux_dir/config.sub"  # Please don't use this var.
 ac_configure="$SHELL $ac_aux_dir/configure"  # Please don't use this var.


-am__api_version='1.15'
+am__api_version='1.13'

 # Find a good install program.  We prefer a C program (faster),
 # so one script is as good as another.  But avoid the broken or
@@ -2499,8 +2487,8 @@ test "$program_suffix" != NONE &&
 ac_script='s/[\\$]/&&/g;s/;s,x,x,$//'
 program_transform_name=`$as_echo "$program_transform_name" | sed "$ac_script"`

-# Expand $ac_aux_dir to an absolute path.
-am_aux_dir=`cd "$ac_aux_dir" && pwd`
+# expand $ac_aux_dir to an absolute path
+am_aux_dir=`cd $ac_aux_dir && pwd`

 if test x"${MISSING+set}" != xset; then
  case $am_aux_dir in
@@ -2519,7 +2507,7 @@ else
 $as_echo "$as_me: WARNING: 'missing' script is too old or missing" >&2;}
 fi

-if test x"${install_sh+set}" != xset; then
+if test x"${install_sh}" != xset; then
  case $am_aux_dir in
  *\ * | *\	*)
    install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
@@ -2813,7 +2801,7 @@ fi

 # Define the identity of the package.
 PACKAGE='stacks'
- VERSION='2.2'
+ VERSION='2.41'


 cat >>confdefs.h <<_ACEOF
@@ -2847,8 +2835,8 @@ MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"}
 # <http://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
 mkdir_p='$(MKDIR_P)'

-# We need awk for the "check" target (and possibly the TAP driver).  The
-# system "awk" is bad on some platforms.
+# We need awk for the "check" target.  The system "awk" is bad on
+# some platforms.
 # Always define AMTAR for backward compatibility.  Yes, it's still used
 # in the wild :-(  We should find a proper way to deprecate it ...
 AMTAR='$${TAR-tar}'
@@ -2864,48 +2852,6 @@ am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'



-# POSIX will say in a future version that running "rm -f" with no argument
-# is OK; and we want to be able to make that assumption in our Makefile
-# recipes.  So use an aggressive probe to check that the usage we want is
-# actually supported "in the wild" to an acceptable degree.
-# See automake bug#10828.
-# To make any issue more visible, cause the running configure to be aborted
-# by default if the 'rm' program in use doesn't match our expectations; the
-# user can still override this though.
-if rm -f && rm -fr && rm -rf; then : OK; else
-  cat >&2 <<'END'
-Oops!
-
-Your 'rm' program seems unable to run without file operands specified
-on the command line, even when the '-f' option is present.  This is contrary
-to the behaviour of most rm programs out there, and not conforming with
-the upcoming POSIX standard: <http://austingroupbugs.net/view.php?id=542>
-
-Please tell bug-automake@gnu.org about your system, including the value
-of your $PATH and any error possibly output before this message.  This
-can help us improve future automake versions.
-
-END
-  if test x"$ACCEPT_INFERIOR_RM_PROGRAM" = x"yes"; then
-    echo 'Configuration will proceed anyway, since you have set the' >&2
-    echo 'ACCEPT_INFERIOR_RM_PROGRAM variable to "yes"' >&2
-    echo >&2
-  else
-    cat >&2 <<'END'
-Aborting the configuration process, to ensure you take notice of the issue.
-
-You can download and install GNU coreutils to get an 'rm' implementation
-that behaves properly: <http://www.gnu.org/software/coreutils/>.
-
-If you want to complete the configuration process using your problematic
-'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM
-to "yes", and re-run configure.
-
-END
-    as_fn_error $? "Your 'rm' program is bad, sorry." "$LINENO" 5
-  fi
-fi
-


 ac_config_headers="$ac_config_headers config.h"
@@ -4163,65 +4109,6 @@ ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
 ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
 ac_compiler_gnu=$ac_cv_c_compiler_gnu

-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC understands -c and -o together" >&5
-$as_echo_n "checking whether $CC understands -c and -o together... " >&6; }
-if ${am_cv_prog_cc_c_o+:} false; then :
-  $as_echo_n "(cached) " >&6
-else
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h.  */
-
-int
-main ()
-{
-
-  ;
-  return 0;
-}
-_ACEOF
-  # Make sure it works both with $CC and with simple cc.
-  # Following AC_PROG_CC_C_O, we do the test twice because some
-  # compilers refuse to overwrite an existing .o file with -o,
-  # though they will create one.
-  am_cv_prog_cc_c_o=yes
-  for am_i in 1 2; do
-    if { echo "$as_me:$LINENO: $CC -c conftest.$ac_ext -o conftest2.$ac_objext" >&5
-   ($CC -c conftest.$ac_ext -o conftest2.$ac_objext) >&5 2>&5
-   ac_status=$?
-   echo "$as_me:$LINENO: \$? = $ac_status" >&5
-   (exit $ac_status); } \
-         && test -f conftest2.$ac_objext; then
-      : OK
-    else
-      am_cv_prog_cc_c_o=no
-      break
-    fi
-  done
-  rm -f core conftest*
-  unset am_i
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_prog_cc_c_o" >&5
-$as_echo "$am_cv_prog_cc_c_o" >&6; }
-if test "$am_cv_prog_cc_c_o" != yes; then
-   # Losing compiler, so override with the script.
-   # FIXME: It is wrong to rewrite CC.
-   # But if we don't then we get into trouble of one sort or another.
-   # A longer-term fix would be to have automake use am__CC in this case,
-   # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
-   CC="$am_aux_dir/compile $CC"
-fi
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-
 depcc="$CC"   am_compiler_list=

 { $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
@@ -4350,6 +4237,131 @@ else
 fi


+if test "x$CC" != xcc; then
+  { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC and cc understand -c and -o together" >&5
+$as_echo_n "checking whether $CC and cc understand -c and -o together... " >&6; }
+else
+  { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether cc understands -c and -o together" >&5
+$as_echo_n "checking whether cc understands -c and -o together... " >&6; }
+fi
+set dummy $CC; ac_cc=`$as_echo "$2" |
+		      sed 's/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/'`
+if eval \${ac_cv_prog_cc_${ac_cc}_c_o+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+# Make sure it works both with $CC and with simple cc.
+# We do the test twice because some compilers refuse to overwrite an
+# existing .o file with -o, though they will create one.
+ac_try='$CC -c conftest.$ac_ext -o conftest2.$ac_objext >&5'
+rm -f conftest2.*
+if { { case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+  (eval "$ac_try") 2>&5
+  ac_status=$?
+  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+  test $ac_status = 0; } &&
+   test -f conftest2.$ac_objext && { { case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+  (eval "$ac_try") 2>&5
+  ac_status=$?
+  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+  test $ac_status = 0; };
+then
+  eval ac_cv_prog_cc_${ac_cc}_c_o=yes
+  if test "x$CC" != xcc; then
+    # Test first that cc exists at all.
+    if { ac_try='cc -c conftest.$ac_ext >&5'
+  { { case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+  (eval "$ac_try") 2>&5
+  ac_status=$?
+  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+  test $ac_status = 0; }; }; then
+      ac_try='cc -c conftest.$ac_ext -o conftest2.$ac_objext >&5'
+      rm -f conftest2.*
+      if { { case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+  (eval "$ac_try") 2>&5
+  ac_status=$?
+  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+  test $ac_status = 0; } &&
+	 test -f conftest2.$ac_objext && { { case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+  (eval "$ac_try") 2>&5
+  ac_status=$?
+  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+  test $ac_status = 0; };
+      then
+	# cc works too.
+	:
+      else
+	# cc exists but doesn't like -o.
+	eval ac_cv_prog_cc_${ac_cc}_c_o=no
+      fi
+    fi
+  fi
+else
+  eval ac_cv_prog_cc_${ac_cc}_c_o=no
+fi
+rm -f core conftest*
+
+fi
+if eval test \$ac_cv_prog_cc_${ac_cc}_c_o = yes; then
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+else
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+
+$as_echo "#define NO_MINUS_C_MINUS_O 1" >>confdefs.h
+
+fi
+
+# FIXME: we rely on the cache variable name because
+# there is no other way.
+set dummy $CC
+am_cc=`echo $2 | sed 's/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/'`
+eval am_t=\$ac_cv_prog_cc_${am_cc}_c_o
+if test "$am_t" != yes; then
+   # Losing compiler, so override with the script.
+   # FIXME: It is wrong to rewrite CC.
+   # But if we don't then we get into trouble of one sort or another.
+   # A longer-term fix would be to have automake use am__CC in this case,
+   # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
+   CC="$am_aux_dir/compile $CC"
+fi
+


      ax_cxx_compile_cxx11_required=true
@@ -5532,12 +5544,6 @@ $as_echo_n "checking the archiver ($AR) interface... " >&6; }
 if ${am_cv_ar_interface+:} false; then :
  $as_echo_n "(cached) " >&6
 else
-  ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
  am_cv_ar_interface=ar
   cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
@@ -5569,11 +5575,6 @@ if ac_fn_c_try_compile "$LINENO"; then :

 fi
 rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-   ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu

 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_ar_interface" >&5
@@ -7416,7 +7417,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by Stacks $as_me 2.2, which was
+This file was extended by Stacks $as_me 2.41, which was
 generated by GNU Autoconf 2.69.  Invocation command line was

  CONFIG_FILES    = $CONFIG_FILES
@@ -7482,7 +7483,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-Stacks config.status 2.2
+Stacks config.status 2.41
 configured by $0, generated by GNU Autoconf 2.69,
  with options \\"\$ac_cs_config\\"


--- a/configure.ac
+++ b/configure.ac
@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.

 AC_PREREQ(2.59)
-AC_INIT([Stacks], [2.2])
+AC_INIT([Stacks], [2.41])
 AC_CONFIG_AUX_DIR([config])
 AM_INIT_AUTOMAKE([-Wall -Werror foreign parallel-tests subdir-objects])
 AC_CONFIG_SRCDIR([src/ustacks.cc])

--- a/debian/NEWS.Debian
+++ b/debian/NEWS.Debian
+stacks (2.41+dfsg-1) unstable; urgency=medium
+
+  * Removed stacks-web package since the code for the web service
+    was removed from upstream source and the package has no active
+    users according to popcon anyway
+
+ -- Andreas Tille <tille@debian.org>  Wed, 10 Jul 2019 21:58:30 +0200
--- a/debian/apache2-conf/stacks-web.conf
+++ b/debian/apache2-conf/stacks-web.conf
-Alias /stacks /usr/share/stacks/php
-
-<Directory /usr/share/stacks/php>
-
-DirectoryIndex index.php
-AllowOverride None
-
-order deny,allow
-deny from all
-# This for local browsing only
-# allow from 127.0.0.0/255.0.0.0 ::1/128
-# Or switch to this for global visibility
-allow from all
-
-<IfModule mod_php5.c>
-  php_flag magic_quotes_gpc Off
-  #php_flag track_vars On
-  #php_value include_path .
-</IfModule>
-<IfModule !mod_php5.c>
-  <IfModule mod_actions.c>
-    <IfModule mod_cgi.c>
-      AddType application/x-httpd-php .php
-      Action application/x-httpd-php /cgi-bin/php
-    </IfModule>
-    <IfModule mod_cgid.c>
-      AddType application/x-httpd-php .php
-      Action application/x-httpd-php /cgi-bin/php
-    </IfModule>
-  </IfModule>
-</IfModule>
-
-</Directory>
--- a/debian/changelog
+++ b/debian/changelog
+stacks (2.41+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * debhelper 12
+  * Standards-Version: 4.4.0
+  * Secure URI in copyright format
+  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+  * dh_auto_install --no-parallel
+  * Removed stacks-web package since the code for the web service
+    was removed from upstream source and the package has no active
+    users according to popcon anyway
+
+ -- Andreas Tille <tille@debian.org>  Wed, 10 Jul 2019 21:58:30 +0200
+
 stacks (2.2+dfsg-1) unstable; urgency=medium

  * New upstream version

--- a/debian/compat
+++ b/debian/compat
-11
+12
--- a/debian/control
+++ b/debian/control
@@ -4,14 +4,14 @@ Uploaders: Tim Booth <tbooth@ceh.ac.uk>,
           Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper (>= 12~),
               python,
               zlib1g-dev,
               libbam-dev,
-               libsparsehash-dev (>= 2.0),
+               libsparsehash-dev,
               samtools,
               libhts-dev
-Standards-Version: 4.2.1
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/stacks
 Vcs-Git: https://salsa.debian.org/med-team/stacks.git
 Homepage: http://creskolab.uoregon.edu/stacks/
@@ -24,6 +24,9 @@ Depends: ${shlibs:Depends},
         samtools,
         libdbi-perl
 Recommends: libspreadsheet-writeexcel-perl
+Conflicts: stacks-web
+Provides: stacks-web
+Replaces: stacks-web
 Description: pipeline for building loci from short-read DNA sequences
 Stacks is a software pipeline for building loci from short-read sequences,
 such as those generated on the Illumina platform. Stacks was developed to work
@@ -32,22 +35,3 @@ Description: pipeline for building loci from short-read DNA sequences
 .
 Note that this package installs Stacks such that all commands must be run as:
 $ stacks <cmdname> <args>
-
-Package: stacks-web
-Architecture: all
-Depends: ${shlibs:Depends},
-         ${misc:Depends},
-         apache2 | httpd,
-         default-mysql-server | virtual-mysql-server,
-         libapache2-mod-php | php-cgi,
-         libdbd-mysql-perl,
-         php-mdb2-driver-mysql
-Recommends: stacks
-Description: web interface for displaying loci from short-read sequences
- Stacks is a software pipeline for building loci from short-read sequences,
- such as those generated on the Illumina platform. Stacks was developed to work
- with restriction enzyme-based data, such as RAD-seq, for the purpose of
- building genetic maps and conducting population genomics and phylogeography.
- .
- This package provides the web-based viewer which you can use to examine Stacks
- output that has been loaded into a MySQL database.
--- a/debian/copyright
+++ b/debian/copyright
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: Stacks
 Upstream-Contact: Julian Catchen <jcatchen@uoregon.edu>
 Source: http://creskolab.uoregon.edu/stacks/

--- a/debian/patches/constants.php.patch
+++ b/debian/patches/constants.php.patch
-Author: Tim Booth <tbooth@ceh.ac.uk>
-Last-Update: Wed, 18 Feb 2015 11:34:22 +0000
-Description: Work together width /usr/sbin/stacks-setup-database
- See README.Debian
-
--- a/php/constants.php.dist
-+++ b/php/constants.php.dist
-@@ -21,8 +21,8 @@
- //
- // Credentials to access Stacks MySQL databases
- //
-$db_user     = "dbuser";
-$db_pass     = "dbpass";
-+$db_user     = "stacksweb";
-+$db_pass     = "stacksweb";
- $db_host     = "localhost";
- 
- //